Distributed system providing dynamic indexing and visualization of genomic data

Abstract

Systems and methods for dynamic visualization of genomic data are provided in which a genomic visualization system adapts presentation of information content according to scale-relevant annotations within a sequence object.

What is claimed is: 
     
       1. A genomic visualization system comprising:
 an indexed genomic database configured to store a sequence object representative of a genomic region, the sequence object comprising a plurality of scale-relevant annotations; and 
 a scaling engine coupled with the indexed genomic data storage and configured to:
 adjust scale-relevant information derived from the scale-relevant annotations of the sequence object as a function of a user selected zoom level; 
 dynamically generate a genomic display object for the sequence object, wherein the genomic display object is representative of the scale-relevant information based on the zoom level, wherein dynamic generation comprises an alteration of presented visualization of the sequence object; 
 wherein the scaling engine dynamically and automatically downsamples data comprising the genomic display object before the downsampled data is transferred to an output device, 
 wherein the scaling engine dynamically and automatically downsamples the data in response to a request that indicates a number of data points that will be utilized by a consuming application, 
 wherein dynamic downsampling is further based on the size of the genomic region requested and knowledge about the graphical resolution of an output device with which the data will be displayed; and 
 transfer the downsampled data to the output device to present the downsampled data comprising the genomic display object to a user. 
 
 
     
     
       2. The system of  claim 1 , wherein the sequence object has a SAM/BAM or BAMBAM format, or wherein the genomic region is one of the following: a whole genome, a chromosome, a chromosomal fragment, and an allele. 
     
     
       3. The system of  claim 1 , wherein downsampling is accomplished by a first mechanism that requires no knowledge of underlying data and uses pre-condensed files and/or a second mechanism that requires additional information about the file type to so dynamically summarize data. 
     
     
       4. The system of  claim 1 , further comprising a bamserver operating as the scaling engine. 
     
     
       5. The system of  claim 4 , further comprising a plurality of bamservers. 
     
     
       6. The system of  claim 1 , further comprising a visualization server operating as the scaling engine. 
     
     
       7. The system of  claim 6 , further comprising a plurality of visualization servers. 
     
     
       8. The system of  claim 1 , wherein the output device comprises at least one of the following: a display, a browser, a printer, a 3D printer, and a speaker. 
     
     
       9. The system of  claim 1 , wherein the scaling engine is further configured to adjust the scale-relevant information by downsampling based on the zoom-level. 
     
     
       10. The system of  claim 9 , wherein the scaling engine is further configured to downsample as a function of data density derived from the zoom-level. 
     
     
       11. The system of  claim 1 , wherein the scaling engine is further configured to determine the zoom level. 
     
     
       12. The system of  claim 11 , wherein the scaling engine is further configured to summarize a full data set of the sequence object according to the zoom level. 
     
     
       13. The system of  claim 1 , wherein the scaling engine is further configured to derive the scale-relevant information from differences in scale-relevant annotations in different sequence objects. 
     
     
       14. The system of  claim 1 , wherein the sequence object comprises a reference sequence object. 
     
     
       15. The system of  claim 14  wherein the reference sequence object is selected from the group consisting of raw sequence data, sequence data from homo statisticus, and sequence data from a specified point in time. 
     
     
       16. The system of  claim 1 , wherein the sequence object comprises a differential sequence object with respect to a reference genomic region. 
     
     
       17. The system of  claim 16  wherein the reference genomic region is from homo statisticus or specific to a point in time. 
     
     
       18. The system of  claim 1 , wherein the scale-relevant annotations include at least one of the following: genomic structure information, genomic change information, disease information, gene relevant information, differential information relative to a reference sequence, and metadata. 
     
     
       19. The system of  claim 18 , wherein the genomic structure includes at least one of the following: chromosome identification, location within a chromosome, and an allele. 
     
     
       20. The system of  claim 18 , wherein the genomic change information includes at least one of the following: a mutation, a translocation, an inversion, a deletion, a repeat, and a copy number. 
     
     
       21. The system of  claim 18 , wherein the disease information includes at least one of the following: a type of disease, a status of disease, and a treatment option for the disease. 
     
     
       22. The system of  claim 18 , wherein the gene relevant information comprises raw sequence data or processed sequence data, gene identification, information on gene regulation, and information of association of the gene with a disease. 
     
     
       23. The system of  claim 18 , wherein the metadata includes at least one of the following: patient identification, facility identification, physician identification, and insurance information. 
     
     
       24. The system of  claim 1 , further comprising a genomic graphic library configured to store a graphic object representative of scale-relevant annotations. 
     
     
       25. The system of  claim 24 , wherein the scaling engine is further configured to map the scale-relevant information to graphic objects from graphic library according to the zoom level. 
     
     
       26. The system of  claim 25 , wherein the genomic display object comprises the mapped graphic objects.